Perl is difficult to learn for beginners without any programming experiment.

Maybe we can paste some code of some basic tasks like reading FASTA sequences to give some examples and encourage beginners to make the first step.

Reading code of others is also an important way of learning programming language.

It's really difficult to debug others' Perl code. Here's a rewritten version with detailed comments.

Seqs:

$ cat dataset1.txt
>1
AAAAAAATGC
ATCGATCGAC
>2
AAAAAAGTCG
ATCGATCAGC

Motifs:

$ cat Motif6.txt
AAAAAA
AAAAAT
AAAAAG
AAAAAC

Code:

#!/usr/bin/env perl
use strict;

# read motifs
my $file_motif = "Motif6.txt";
my @motifs = (); # an array to store motifs
open my $fh, "<", $file_motif or die "fail to open file: %file_motif";
for my $line (<$fh>) {
    $line =~ s/\r?\n//g;    # chomp "\r" and "\n"
    next if $line eq "" or $line =~ m/\s+/; # skip blank line
    push @motifs, $line; # append to array
}
close $fh;

# read sequences and count motifs
my $file_seq = "dataset1.txt";
my %counter = (); # a hashmap to store countings

open my $fh, "<", $file_seq or die "fail to open file: $file_seq";
my ($header, $seq) = ("", "");
for my $line (<$fh>) {
    $line =~ s/\r?\n//g; # chomp "\r" and "\n"
    if (substr( $line, 0, 1 ) eq '>') { # FASTA header line
        unless ($header eq "" and $seq eq "") { # previous sequence
            &count_motifs($header, $seq);
        }

        $header = substr ($line, 1); # update header
        $seq = ""; # reset seq
    } else { # sequence line
        $seq = $seq . $line # concatenate sequence
    }
}
close $fh;

unless ($header eq "" and $seq eq "") { # do not forget the last sequence
    &count_motifs($header, $seq);
}

# print result, in decending order of count
for my $motif (sort {$counter{$b} <=> $counter{$a}} keys %counter) {
    print "$motif\t$counter{$motif}\n";
}

sub count_motifs {
    my ($header, $seq) = @_;
    for my $motif (@motifs) {
        my $n = 0;
        my $len_motif = length $motif;
        my ($begin, $end) = (-1, -1);

        # if you just want to test whether the seq contains a motif, use:
        $n++ if $seq =~ m/$motif/i;

        # if you want to find all matches in sequences, use:
        # while ($seq =~ m/$motif/gi) { # use regular expression to locate motifs
        #     my $pos = pos $seq; # http://perldoc.perl.org/functions/pos.html
        #     ($begin, $end) = ($pos - $len_motif + 1, $pos);
        #     print STDOUT "seq: $header\tmotif: $motif\tlocation: $begin-$end\n";
        #     pos $seq = $pos - $len_motif + 1;
        #     $n++;
        # }

        $counter{$motif} += $n;
    }
}

Result:

$ perl count_motifs_in_seqs.pl
AAAAAA  2
AAAAAG  1
AAAAAT  1
AAAAAC  0

Some comments:

• As others have pointed out: use strict; use warnings
• Your program processes fasta files correctly, if and only if they contain
  • exactly one line of sequence per 1 line of header
  • no blank lines, while your fasta reading by reading into a hash looks like a neat hack, fasta files cannot be read correctly like this.
• The minimum for any file parsing is at least to chomp, and to skip blank lines. That also applies to your Motif file where you have blank lines, and they will be searched in the sequence.
• Do not use C style for loops with incremental counters to iterate, use an iterator instead: foreach or map
• Pattern matching: what to count if a motif matches a pattern multiple times?

• Logic of counting and iteration does not combine, you defined only a global counter, but your loop logic does not fit to this. You can easily see that the following code will output an ever increasing number for each combination of motif and target sequence:

  # this is pseudocode of what you are trying:
  0: counter := 0
  1: forall target in target sequences 
  2:   forall motif in motifs
         if (motif matches target): 
             increment (counter)
         print "motif occurs in" counter "sequences at least once (NOT)"
  

You need to change the sequence of loop control in line 0-2 to suit your problem (hint: 2,0,1 looks like a good sequence)

Check this post counting motifs in dna sequence, no programming needed. You might skip the step 1.

You can use hash to store your motif,and the values are the numbers of motif.If match one motif,Its value should +1.

#! /usr/bin/env perl
open IN,"PATH" || die "$!";
#AAAAAAATGCATCGATCGAC
#AAAAAAGTCGATCGATCAGC
open MOTIF,"PATH" || die "$!";
#AAAAAA
#AAAAAT
#AAAAAG
#AAAAAC
%motif=();
while(defined($t=<MOTIF>)){
    chomp($t);
    $motif{$t}=0;
}
while(defined($line=<IN>)){
    chomp($line);
    foreach (keys %motif){
        my $count=$line=~m/$_/;
        $motif{$_}+=$count;
    }
}
@motif=keys %motif;
foreach (@motif){
    print "$_\t$motif{$_}\n";
}
close IN;
close MOTIF;

And the result:

AAAAAG  1
AAAAAT  1
AAAAAA  2
AAAAAC  0